BACKGROUND: The COVID-19 pandemic led to dramatic changes in the lives of children that impact cardiometabolic health. Cities and counties had varying policies with respect to school closure, recreational programs, and efforts to mitigate food insecurity and economic distress. Our objective was to evaluate changes in BMI-z score and prevalence of overweight/obesity prior to and during the pandemic among children in San Francisco, CA, where public schools were closed for 18-months. METHODS: This was an electronic medical record-based retrospective cohort study. We included 15,401 children, 4-17 years of age at study onset. Our exposure was time into each of three time periods: (1) March 2018-February 2019; (2) March 2019-February 2020; (3) March 2020-August 2021 (the pandemic period of school closure). Generalized estimating equations (GEE) were used to assess changes in BMI-z score and overweight/obesity across the three time periods. We assessed for effect modification by age-category, insurance status, and race/ethnicity. RESULTS: Mean BMI-z score increased by 0.06 per year in time period 2, the year prior to the pandemic (p < 0.001, 95% CI: 0.04, 0.09), and by 0.12 per year during time period 3, the first 18 months of the pandemic (p < 0.001, 95% CI 0.10, 0.13). The proportion of children with overweight/obesity increased by 1.4% points per year during time period 2 (p = 0.012, 95% CI: 0.03, 2.46) and by 4.9% points per year during the first 18 months of the pandemic (p < 0.001, 95% CI: 4.11, 5.67). The effect modification analysis demonstrated that the youngest age group, publicly insured children (versus privately insured), and Black, Latino, and Asian children (versus White children) experienced greater increases in BMI-z score during the pandemic (p < 0.01 for all comparisons). The youngest age group (p = 0.022) and publicly insured children (versus privately insured children) (p < 0.001) also experienced greater increases in the proportion of children with overweight/obesity during the pandemic. CONCLUSIONS: Among children in San Francisco, increases in BMI-z score and overweight/obesity were greater during the pandemic compared to prior changes, with the most pronounced increases among younger and publicly insured children. These findings support the need for more targeted and effective policies for addressing childhood overweight/obesity, especially among these high-risk populations.